Gene: YBX2

LinkedOmicsKB © 2022-2023 Zhang Lab

Basic information

Full name
Y-box binding protein 2
Ensembl
ENSG00000006047.13
Summary
This gene encodes a nucleic acid binding protein which is highly expressed in germ cells. The encoded protein binds to a Y-box element in the promoters of certain genes but also binds to mRNA transcribed from these genes. Pseudogenes for this gene are located on chromosome 10 and 15. [provided by RefSeq, Feb 2012]
Annotation
Transcription factor

Protein product

Phosphosites on the primary protein product

Tumor and normal comparison

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Signed p-values
Data type
Meta P
BRCA
CCRCC
COAD
GBM
HNSCC
LSCC
LUAD
OV
PDAC
UCEC
RNA1.5e-6--0.92---7.6e-71.8e-235e-16--0.61-
protein4.7e-4-2.8e-4-2.5e-5--0.996.4e-75.8e-4---

* P-values are from Wilcoxon rank sum test and can be clicked to show the box plots. Positive values mean higher abundance in tumor. BRCA and GBM do not have normal samples.

mRNA expression at gene level
BRCACCRCCCOADGBMHNSCCLSCCLUADOVPDACUCEC012345678910log2(RSEM+1)tumornormal
Protein expression
BRCACCRCCCOADGBMHNSCCLSCCLUADOVPDACUCEC1516171819202122232425262728log2(MS1 intensity)tumornormal

* Mild outlier: filled circle; Extreme outlier: empty circle.

Phenotype and mutation association

Manhattan plot summarizing associations of phenotypes and mutations across all cohorts and omics data types

BRCACCRCCCOADGBMHNSCCLSCCLUADOVPDACUCEC0123456789101112130-1-2-3-4-5-6-7-8-9-10-11-12-13Pan-cancer02468101214160-2-4-6-8-10-12-14-16proteinRNASCNVclinicalpathwaycell typegenomicmutation-log10 of P-value

* Data points of significant associations above and below the dotted lines can be hovered to show the phenotype.

Associations of the protein abundance of YBX2 with phenotypes and mutations

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Signed p-values
Phenotype
Meta P
BRCA
CCRCC
COAD
GBM
HNSCC
LSCC
LUAD
OV
PDAC
UCEC
HALLMARK_G2M_CHECKPOINT6.9e-80.0270.250.30.280.282.8e-41.2e-3-0.99-0.211.1e-6
HALLMARK_E2F_TARGETS1.3e-60.060.180.860.12-0.928.3e-43.5e-30.96-0.25.4e-8
chromosomal instability5.2e-50.0660.45-0.680.570.190.0033.2e-30.3-0.440.01
HALLMARK_MYC_TARGETS_V25.7e-50.0370.550.810.7-0.383.7e-37.5e-30.21-0.432.2e-5
HALLMARK_SPERMATOGENESIS1.1e-40.12-0.3-0.70.170.71.2e-40.0270.79-0.618.2e-6
KINASE-PSP_CDK11.7e-40.003-0.110.140.290.860.0380.012-0.30.493.2e-4
xcell: T cell CD4+ Th11.9e-40.60.580.90.52-0.552.6e-31.9e-30.023-0.412.8e-3
Tumor Purity (ABSOLUTE)4.8e-40.0610.35-0.810.320.290.0160.0390.220.660.78
TP53 mutation6.1e-40.059-0.52---0.058--0.015
KINASE-PSP_CDK29.5e-40.03-0.430.290.170.458.1e-30.046-0.091-0.351.1e-4
Showing 1 to 10 of 256 rows

* P-values could be from test for Spearman correlation, Wilcoxon rank sum test, Jonckheere-Terpstra trend test or Cox regression depending on the data type. P-values for individual cohorts can be clicked to show the data plots. The matrix icons in each row can be clicked to show a heatmap summary of associations across all cohorts and omics. The rows in the table can be expanded to show results from other omics.

Cis-association

Associations between omics data of YBX2

BRCA0.820.230.17proteinmRNASCNVmethylationCCRCC0.130.09-0.01-0.270.05-0.09proteinmRNASCNVmethylationCOAD0.490.190.12proteinmRNASCNVmethylationGBM0.68-0.140.150.10-0.15-0.23proteinmRNASCNVmethylationHNSCC0.12-0.07-0.03-0.32-0.06-0.09proteinmRNASCNVmethylationLSCC0.69-0.220.07-0.150.05-0.24proteinmRNASCNVmethylationLUAD0.67-0.170.10-0.14-0.02-0.10proteinmRNASCNVmethylationOV0.670.210.24proteinmRNASCNVmethylationPDAC0.25-0.050.27-0.16-0.04-0.24proteinmRNASCNVmethylationUCEC0.81-0.17-0.09-0.34-0.040.09proteinmRNASCNVmethylation

* The numbers are Spearman correlation coefficients and can be clicked to show the scatter plots. The color and size of the circles correlate with the coefficients.

Trans-association

Associations of the protein abundance of YBX2 and the protein abundance of other genes

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Signed p-values
Gene
Meta P
BRCA
CCRCC
COAD
GBM
HNSCC
LSCC
LUAD
OV
PDAC
UCEC
No matching records found

* P-values are from test for Spearman correlation. P-values for individual cohorts can be clicked to show the data plots. The matrix icons in each row can be clicked to show a heatmap summary of associations across all cohorts and omics. The rows in the table can be expanded to show results from other omics.

Gene set enrichment analysis

Submit genes and the common logarithm of the p-values of their association with to WebGestalt.